variant sites ?

[ling]

Hi :

I have a question about the report of populations program. At the end of the run, the final log file will have some results.

variant sites is SNP, polymorphic sites is SNP+Indel...? but the number of polymorphic sites is less than snp, I don't quite understand how to be sure it.

Thanks a lot

ling

[Catchen, Julian]

Hi Ling,

 

Variant sites is any site that is polymorphic in at least one population. A polymorphic site is a SNP in the focal population. Indels are not explicitly counted among those two categories.

 

julian

[Hu Ling]

Hi  Julian:

Thanks for your reply!

That is , the  variant site are SNP common to all or several populations, while the polymorphic site are SNP within a single population, right?

Thanks

ling

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